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1.) First off, is there any benefit to loading up my case with fans? I want to dust my PC out as little as possible and maximize airflow.
Yes, if you use all the 8 fans, the system will be cooler, but the temp will not drop a lot. If you want to less dust inside the case, then you need use the positive pressure configuration, but you will not get the best cooling performance in this way, for more info check the link
http://www.extremetech.com/computing/128313-extremetech...
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2.) Does having an intake fan on the bottom fan slot have any advantage/benefits?
Yes, you will get more cooling benefits because you want the cool air comes in the case from lower front / bottom, and let the hot air exhaust from top/rear, but I think the 200R does not have the filter in that area so that it is not a good idea to use.
Your MB has 3X cha-fan headers, one is next the 24pin power header, one is near the SATA port, and one is next the audio connector for the back panel. If you have 6 fans ( 2 from case, you bought 4 of them) then you can get more the fan splitter. The cpu_opt header is intended for a secondary CPU fan, in theory you can use it. If you want less dust inside your case, then I recommend to use two fans (intake) in front and connect them into the cha-fan header that is next the 24pin power header. One fan (intake) is in the side panel, to connect it on the one near the SATA port, and you use the cha_fan ( next the audio) header for one rear fan + one top fan ( both exhaust ) . If you use the fan splitter on the cpu-fan header, it does not work you have to use the cpu_fan and the cpu_opt if you have two fans for the cpu cooler.
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5.) Why does the fan power splitter have three pins on one side and four on the other (see Newegg photo for reference)?
It is only one of the fan splitter, there is other type of the splitter too, like this
http://www.kenable.co.uk/images/k-PMW-FAN-SPLITTER.jpg
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6.) If I decide to put a fan on the bottom for intake, I'll likely need some kind of adapter to power it. What kind of adapter would I need? I assume I could use a spare legacy molex power adapter from my PSU but would that mean I need a molex - fan power adapter?
If there is not filter you are better don't use, if you want get the other splitter then you can connect it with the side panel fan. Or get the 3-pin Fan to 4-pin adapter to connect to the PSU 4 pin molex.
http://www.newegg.com/Product/Product.aspx?Item=N82E168...
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7.) I understand if no one will be able to answer this but my case has the option for a second fan underneath the pre-installed front case fan. The only thing is the place where this second fan is supposed to go is right where the HDD bays are so I don't understand how it's supposed to fit there.
You may need take off the front panel to install the fan.
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8.) My current CPU cooler leaves almost no room for a second side fan - any recommendations on a super slim fan?
You are better to don't it because it will cause turbulence, hindering the efficient flow of air through a case. But you can use the other one for the GPU.
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9.) Lastly, will these fans eat up much power? I'm currently using about ~423 watts on a 650W PSU with my current setup without the added fans.
The fan can't draw too much power, you can calculate Watt=V X Amp, when you check the fan like the CM one you can see it has the 12V with 0.16A on the label, so it is only draw 1.92W. So you are fine, also most of MB fan header can output about 1 amp so you are fine to use the fan splitter too. And you can use the ASUS fan xperts to control the fans speed.